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- PDB-6s99: Dimethylated fusion protein of RSL and trimeric coiled coil in co... -

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Basic information

Entry
Database: PDB / ID: 6s99
TitleDimethylated fusion protein of RSL and trimeric coiled coil in complex with cucurbit[7]uril
Components4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / fusion protein / molecular glues / crystal engineering / cucurbituril
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-mannopyranose / cucurbit[7]uril / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.649 Å
AuthorsRamberg, K. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland Ireland
CitationJournal: Chemistry / Year: 2021
Title: Segregated Protein-Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons.
Authors: Ramberg, K.O. / Guagnini, F. / Engilberge, S. / Wronska, M.A. / Rennie, M.L. / Perez, J. / Crowley, P.B.
History
DepositionJul 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_atoms.polymer_flag / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
B: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
C: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
D: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
E: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
F: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,38924
Polymers74,2496
Non-polymers9,14018
Water2,018112
1
A: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
B: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
C: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,69412
Polymers37,1243
Non-polymers4,5709
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-12 kcal/mol
Surface area17350 Å2
MethodPISA
2
D: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
E: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
F: 4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,69412
Polymers37,1243
Non-polymers4,5709
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-8 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.219, 51.242, 111.282
Angle α, β, γ (deg.)76.80, 89.88, 60.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
4dzn-RSL,Fucose-binding lectin protein,Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 12374.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, HF909_06975, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M TRIS HCL pH 8.5, 20% PEG8000, 0.2 M Magnesium Chloride, 0.0013 M cucurbit[7]uril

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.649→42.842 Å / Num. obs: 26787 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Net I/σ(I): 7.8
Reflection shellResolution: 2.649→2.695 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1383 / Rpim(I) all: 0.19

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.649→42.842 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 30.06
RfactorNum. reflection% reflection
Rfree0.2565 1410 5.27 %
Rwork0.2245 --
obs0.2262 26777 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.649→42.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 690 112 5590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135730
X-RAY DIFFRACTIONf_angle_d1.3648130
X-RAY DIFFRACTIONf_dihedral_angle_d13.5322178
X-RAY DIFFRACTIONf_chiral_restr0.098834
X-RAY DIFFRACTIONf_plane_restr0.0271194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6492-2.74390.34481020.31352549X-RAY DIFFRACTION98
2.7439-2.85380.36991240.30242663X-RAY DIFFRACTION98
2.8538-2.98360.33051770.28372450X-RAY DIFFRACTION98
2.9836-3.14090.28391400.24982557X-RAY DIFFRACTION98
3.1409-3.33760.29961760.22692480X-RAY DIFFRACTION98
3.3376-3.59520.24131260.22992581X-RAY DIFFRACTION97
3.5952-3.95670.20551240.20032540X-RAY DIFFRACTION97
3.9567-4.52870.20481490.19652470X-RAY DIFFRACTION96
4.5287-5.70360.21511840.20172527X-RAY DIFFRACTION97
5.7036-42.8480.33921080.23132550X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -0.7799 Å / Origin y: 0.1014 Å / Origin z: -1.2297 Å
111213212223313233
T0.3032 Å20.0001 Å20.0113 Å2-0.3153 Å2-0.0029 Å2--0.5122 Å2
L1.1486 °2-0.0099 °20.0812 °2-1.0876 °2-0.0652 °2--1.9167 °2
S0.0311 Å °-0.0056 Å °0.0184 Å °0.0039 Å °0.0278 Å °0.0036 Å °-0.0007 Å °0.002 Å °0.0051 Å °
Refinement TLS groupSelection details: all

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